Species, geography, and weather conditions predict offshore migration in songbirds

Autumn Routing Content Data data/: Contains processed data and information on false positive detections. app.R: Shiny app for filtering false positives and data validation. data_flights-*.csv: Processed data ready for analysis containing information on individual flights and weather data. flightpaths-*.csv: Estimated locations for individual flights paths. recvDeps.csv: Receiver station deployments. tagDeps.csv: Tag deployments. Code main.R: Run the complete analysis pipeline. R/: Contains all the R code to run the analysis. _setup.R: Configure the project environment. _utils.R: Utility functions. 1_data_preparation.R: Process telemetry data downloaded from Motus. 2_maps.R: Generate maps of the flight tracks. 3_multi-state.R: Analyse departure decision using a multi-state model. 4_mixture_simulation.R: Simulate and analyse flight distance using the generative mixture model. 5_mixture_modelling.R: Analyse flight distance using the same mixture model. Stan/: Contains Stan code for the models. Documentation vignettes/: Contains vignettes for the analysis. supplement.qmd: Supplementary materials. Manuscript index.qmd: Manuscript source file. figures/: Contains visual assets that are embedded in the manuscript. results/: Contains data objects generated by the research pipeline. Utility bibtexDOI.sh: Bash script that fetches the BibTeX entry for a given DOI and appends it to the project bibliography file. Reproducibility This project was conducted with R 4.5.2 and leverages renv to ensure a reproducible R environment. The renv package captures and restores the exact package versions used in this analysis, enabling others to recreate the environment precisely. Download this archive or clone the Git repository: git clone https://codeberg.org/migecol/autumn_routing Open the project in your preferred editor. In the project’s working directory, restore the environment using renv: install.packages("renv") renv::restore() When prompted, select “1: Activate the project and use the project library”. This will install all required packages as specified in the renv.lock file. Run the analysis.